Job Scheduler

A simple script which logs the CPU and RAM usage of the submitted job

ClusterMonitor

A very simple python script which monitors and records the CPU and RAM consumption of submitted cluster jobs.

Usage

To start recording use the cpu_ram_log.py script. This script requires 3 arguments:

  • -u which corresponds to your username.
  • -o which specifies the output file (in tsv format)
  • --interval which specifies the time (in seconds) over which the CPU and RAM usage gets averaged

Example:

python cpu_ram_log.py -u nickhir -o cpu_ram.log --interval 5

The script can simply be included in your cluster job submittion like this:

#!/bin/bash
#SBATCH --job-name=Example_run

sambamba sort -t 20 some_bam.bam &
MainScript=$!
python cpu_ram_log.py -u nickhir -o cpu_ram.log --interval 5 &
wait $MainScript
pkill -P $$

Afterwards the resulting log file can be plotted (for that matplotlib is

 

 

 

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